A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers

PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2BD ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.Communicated by Ramaswamy H. Sarma.

Effects of restraint parameters using PIPER 6y in reclined seating during frontal impact

OBJECTIVE

This study explores possible challenges for child occupants in reclined seating positions, applying current protection systems. Using PIPER 6 y in frontal impacts, the aim was to investigate the effect of restraint parameters in reclined seating positions, in addition to an upright position, varying booster design, shoulder belt outlet, and pretensioner activation.

METHOD

Eighteen full frontal impacts were simulated using the PIPER 6 y human body model restrained on a booster in a front passenger seat. The type of booster, pretensioner activation and shoulder belt outlet were varied with the vehicle seat in 'upright position' (25°) and 'reclined position' (40°). Three booster principles were used: booster seat (BoosterA), booster cushion (BoosterB) and representing properties of a vehicle built-in booster cushion (BoosterC). The two shoulder belt outlets include 'nominal D-ring' and 'rearward D-ring´.

RESULTS

Overall, activation of the pretensioner reduced the overall body displacement as well as the head and neck response in both seating positions. Submarining occurred only in the case of BoosterB in 'reclined position' without pretensioner. Some differences were observed for the lap belt interaction with pelvis in the non-submarining simulations. Greater pelvis displacement was observed in 'reclined position' as compared to 'upright position'. In both seating positions, greatest pelvis displacement was observed for BoosterB, due to relatively more forward initial lap belt position. While both provided favorable initial lap belt to pelvis contact, BoosterC offered more efficient lap belt restraint than BoosterA, since the lap belt remained lower on the pelvis and the vertical movement of the pelvis was more limited compared to BoosterA. When in 'reclined position', the 'rearward D-ring' position enabled earlier coupling of the torso due to initial shoulder belt to shoulder contact, resulting in lower head and neck responses as well as shorter head displacement compared to 'nominal D-ring'.

CONCLUSIONS

Submarining can be addressed in reclined seating positions using current booster design in combination with a seatbelt pretensioner. Lap belt routing was influenced by booster design and reclined seating, affecting the overall kinematics and responses of the PIPER 6 y. This study highlights the importance of including the whole context of child occupant protection when investigating reclined seating, such as the interaction and compatibility of booster, vehicle seat and seatbelt.

Booster cushion design effects on child occupant kinematics and loading assessed using the PIPER 6-year-old HBM and the Q10 ATD in frontal impacts

OBJECTIVE

Our objective was to study the effect on child occupant kinematics and loading by differences in booster cushion designs and attachment in a frontal impact.

METHODS

Three different booster cushion designs were exposed to a frontal impact in vehicle rear seat interiors. The boosters were selected based on their difference in shape, stiffness, and guiding loop design. Tests were run varying the shoulder belt routing above or under the guiding loop, in addition to with or without attachment of the booster cushion to the vehicle ISOFIX anchorages. Eighteen simulations with the finite element PIPER 6-year-old human body model (HBM) were run investigating all combinations of parameters, in addition to 3 sled tests with a Q10 anthropomorphic test dummy (ATD).

RESULTS

Across 2 different child sizes, using an HBM and an ATD, respectively, consistent sensitivity to the booster design differences were seen. Boosters providing similar initial static belt fit can result in different occupant responses during a crash, due to the design of the boosters and their dynamic performance. Compression of the booster cushion resulted in a delayed pelvis restraint, influencing the upper body kinematics. The guiding loop design as well as the belt routing above or under the guide also influenced the upper body kinematics and shoulder belt interaction.

CONCLUSIONS

Early pelvis coupling to initiate torso pitch, and thereby an upper torso motion controlled by the shoulder belt, is the preferred occupant protection for booster-seated children. A stable mid-shoulder belt position centered over the chest initially is a prerequisite. Additionally, it was seen that the design of the guiding loops helps provide favorable interaction with the torso during the crash. The option to allow the shoulder belt to be placed above and under the guiding loops will accommodate a larger span of child sizes and adapt to more vehicle seat belt geometries. This study provides evidence that the design of the booster cushion plays an important role in creating an early pelvis coupling, as well as supporting favorable torso-shoulder belt interaction.

Evaluating the response of the PIPER scalable human body model across child restraining seats in simulated frontal crashes

OBJECTIVE

Booster seats ensure appropriate belt fit for children that a traditional vehicle seat belt cannot offer to small occupants. In this study, the responses of the PIPER 6-year-old human body model are compared to the traditional Q6 anthropomorphic test dummy (ATD).

METHODS

Eight frontal impact finite element simulations were run using 4 different child restraining systems on the FMVSS 213 test bench. Kinematics and kinetics were extracted and compared between the 2 child models.

RESULTS

The PIPER 6-year-old showed variation by 11.2 ± 14.1% (head resultant acceleration, G), 20.4 ± 50.3% (chest resultant acceleration, G), 272.9 ± 188.4% (chest displacement, mm), 24.8 ± 17.5% (maximum head excursion, mm), -31.5 ± 5.1% (neck force, F_z, N), -73.8 ± 2.8% (neck moment, M_y, N.m), and -60.4 ± 7.2% (N_ij) compared to the Q6. However, the kinematics of both models were nearly similar.

CONCLUSIONS

The PIPER model has a flexible neck and shows higher chest displacement compared to the Q6. We hypothesize that this is due to the inherent anatomical and mechanical differences between the human body model and the ATD model. More research is needed to explore these differences systematically.

Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition

The telomere G-quadruplex-binding and telomerase-inhibiting capacity of two cationic (TMPyP4 and PIPER) and two anionic (phthalocyanine and Hemin) G-quadruplex-ligands were examined under conditions of molecular crowding (MC). Osmotic experiments showed that binding of the anionic ligands, which bind to G-quadruplex DNA via π-π stacking interactions, caused some water molecules to be released from the G-quadruplex/ligand complex; in contrast, a substantial number of water molecules were taken up upon electrostatic binding of the cationic ligands to G-quadruplex DNA. These behaviors of water molecules maintained or reduced the binding affinity of the anionic and the cationic ligands, respectively, under MC conditions. Consequently, the anionic ligands (phthalocyanine and Hemin) robustly inhibited telomerase activity even with MC; in contrast, the inhibition of telomerase caused by cationic TMPyP4 was drastically reduced by MC. These results allow us to conclude that the binding of G-quadruplex-ligands to G-quadruplex via non-electrostatic interactions is preferable for telomerase inhibition under physiological conditions.